From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Fri Jul 03 2015 - 09:08:25 CDT
Then you've misunderstood it. Don't use impropers. This isn't an
improper that you are restraining, but instead the 6 dihedral angles
that contribute to the pucker.
-Josh
On 07/02/2015 12:35 PM, Lara rajam wrote:
> Dear NAMD !
>
> Thank you for the reply , I am using a amber parameter file, and would
> like to run the MD using NAMD .
> I would like to fix the puckering with the force constant to be 2
> kcal/mol.
> is it possible to do this .
>
> What i have understood from this is the k and ref one need to give
> and i should only use the improper tag.
> one more clarification is , the NAMD says the atom record is from 0
> and i am using the amber file there it starts from 1 ., if some one
> who has carried out this kind of simulation can give me some
> explanations it will be useful to understand more
>
> thanks in advance !
>
>
>
>
>
> On Thu, Jul 2, 2015 at 10:48 AM, Josh Vermaas <vermaas2_at_illinois.edu
> <mailto:vermaas2_at_illinois.edu>> wrote:
>
> Hi Lara,
>
> I think you would benefit from reading up a bit more on the CHARMM
> force field, and what the individual terms mean. The NAMD tutorial
> has some more detailed explanations
> (http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-win-html/node26.html#bondstretch
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_Training_Tutorials_namd_namd-2Dtutorial-2Dwin-2Dhtml_node26.html-23bondstretch&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=m8h_x9pzA3Uuh-pu_LGODSKgyjkq-37Pa2PICgGBVwY&s=1bi4sxn47yrmup-C0-bpXbAsejH-amWTTvCV64axhwA&e=>,
> http://www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/forcefield-html/node5.html
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_Training_Tutorials_science_forcefield-2Dtutorial_forcefield-2Dhtml_node5.html&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=m8h_x9pzA3Uuh-pu_LGODSKgyjkq-37Pa2PICgGBVwY&s=ZPnuqgJ_m0ihkKf8ujcN5jwvljyrne-ZoOEUrxzid1M&e=>),
> but basically you will want to use the first specification, since
> you want to keep the sugar at a specific pucker, which can be done
> with harmonically constrained dihedral angles going around the
> ring (ie. the potential you want to add is like k*(phi-ref)^2).
> The second specification is if you want to add another
> k*(1+cos(n*phi-ref)) potential term. Impropers are "fake"
> dihedrals that do not describe rotation about a bond, and are
> usually used to keep a planar part of the molecule planar.
>
> The size of k depends on how big of a tolerance you have for
> deviations from the ideal geometry. kT at room temperature is ~0.6
> kcal/mol. How much deviation are you willing to tolerate when you
> run your simulation?
>
> -Josh Vermaas
>
>
> On 07/02/2015 09:20 AM, Lara rajam wrote:
>> Dear NAMD users !
>>
>> I would like to fix the sugar puckering during the simulation.
>> how it should be done in NAMD , do i need to use the dihedral or the
>> improper flag in the extra bonds.
>>
>> I have read through and got information like
>>
>> * dihedral <atom> <atom> <atom> <atom> <k> <ref>
>> * dihedral <atom> <atom> <atom> <atom> <k> <n> <ref>
>> * improper <atom> <atom> <atom> <atom> <k> <ref>
>> * improper <atom> <atom> <atom> <atom> <k> <n> <ref>
>>
>> my question is K refers to the spring constant , what should be the
>> value given to it and what does the other flag n refer to .
>>
>> if more information is given it will improve my understanding !
>>
>> thank you !
>
>
This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:21:12 CST